o— author: Guillaume Chomicki1*, Gustavo G. Burin2, Toby ??, Susanne S. Renner3 title: The effects of mutualism on trait evolution - Residuals from ClimPC output: pdf_document: toc: true extra_dependencies: [“float”] latex_engine: xelatex keep_tex: true html_document: toc: true toc_float: true header-includes: -

Submitted to Ecology Letters, Evolution or Evolution Letters – well let’s see what we find!

Affiliations: 1Department of Bioscience, Durham University, Stockton Rd., Durham DH1 3LE, UK. 2University of Sao Paulo, xxxxx. 3Systematic Botany and Mycology, Department of Biology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany.

Correspondence: *

Analyses accounting for climate

The results below follow the same rationale as the ones from the main document. However, in the cases below all analyses use the plant traits already accounted for climatic effects by using the residuals from the regressions between each trait and the first three Principal Components of the climatic variables obtained from BioClim (REF).

Methods

here::i_am("manuscript/chomicki_et_al_climpc.Rmd")

source(here::here("R/tree_plots.R"))
library("knitr")
library("RColorBrewer")
library("kableExtra")
# load("../output/first_analysis.RData")
knitr::opts_chunk$set(fig.pos = "h", out.extra = "")
# source("../R/ouwie_summary_mcc.R")
pars.table.pc1 <- read.csv(here::here("output/fullpar_table_climpc1.csv"))
pars.table.pc1$trait <- c("Stem Area", "Leaf Area", "Corola Length", "Petiole Length", "Hole Diameter")[match(pars.table.pc1$trait, c("stemarea", "leafarea", "corleng", "petleng", "holediam"))]
pars.table.pc2 <- read.csv(here::here("output/fullpar_table_climpc2.csv"))
pars.table.pc2$trait <- c("Stem Area", "Leaf Area", "Corola Length", "Petiole Length", "Hole Diameter")[match(pars.table.pc2$trait, c("stemarea", "leafarea", "corleng", "petleng", "holediam"))]
pars.table.pc3 <- read.csv(here::here("output/fullpar_table_climpc3.csv"))
pars.table.pc3$trait <- c("Stem Area", "Leaf Area", "Corola Length", "Petiole Length", "Hole Diameter")[match(pars.table.pc3$trait, c("stemarea", "leafarea", "corleng", "petleng", "holediam"))]
colors <- setNames(brewer.pal(4, "Set1"), 1:4)
sig.formatter <- function(x){cell_spec(x, format = "latex", bold = ifelse(x > 75, TRUE, FALSE), background = if(x >= 90){"red"} else if(x < 90 & x >= 50){"yellow"})}

MCC tree

Results

Ancestral State Reconstruction of Mutualistic Strategy

The following figure represents the summary of 1000 stochastic maps for each discrete trait, that were summarized for each node.

Evolution of continuous traits based on states of discrete traits

Lastly, we fitted all 7 models of leaf area evolution to 10 sampled evolutionary histories of mutualistic strategy. Due to the elevated number of variables and models, we opted to use a model averaging approach by calculating the weighted average of parameter values. The final value of each parameter was calculated by multiplying the estimated value for a given parameter in a given model by the Akaike weight of the given model. Thus, we need not resort to any arbitrary criterium (such as \(\delta\)AIC > 2) and can evaluate the dynamics solely based on the parameter values.

All plots below were filtered to exclude parameter values that were larger than -10 (\(e^-10\)) and smaller than 10 (\(e^10\)), on the justification of representing bad fitting or unreasonable biological meaning.

Appendages

PC1 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Appendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Appendage.

PC1 - Parameter differences

PC2 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Appendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Appendage.

PC2 - Parameter differences

PC3 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Appendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Appendage.

PC3 - Parameter differences

Architecture

PC1 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Archendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Archendage.

PC1 - Parameter differences

PC2 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Archendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Archendage.

PC2 - Parameter differences

PC3 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Archendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Archendage.

PC3 - Parameter differences

Domatium Growth

PC1 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Domgrowendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Domgrowendage.

PC1 - Parameter differences

PC2 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Domgrowendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Domgrowendage.

PC2 - Parameter differences

PC3 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Domgrowendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Domgrowendage.

PC3 - Parameter differences

Leaf Structure

PC1 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Leafstrucendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Leafstrucendage.

PC1 - Parameter differences

PC2 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Leafstrucendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Leafstrucendage.

PC2 - Parameter differences

PC3 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Leafstrucendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Leafstrucendage.

PC3 - Parameter differences

Mating System

PC1 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Matsysendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Matsysendage.

PC1 - Parameter differences

PC2 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Matsysendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Matsysendage.

PC2 - Parameter differences

PC3 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Matsysendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Matsysendage.

PC3 - Parameter differences

Reward

PC1 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Rewardendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Rewardendage.

PC1 - Parameter differences

PC2 - Parameter

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Rewardendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Rewardendage.

PC2 - Parameter differences

PC3 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Rewardendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Rewardendage.

PC3 - Parameter differences

Strategy

PC1 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Strategyendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Strategyendage.

PC1 - Parameter differences

PC2 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Strategyendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Strategyendage.

PC2 - Parameter differences

PC3 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Strategyendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Strategyendage.

PC3 - Parameter differences

Warts

PC1 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Wartsendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Wartsendage.

PC1 - Parameter differences

PC2 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Wartsendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Wartsendage.

PC2 - Parameter differences

PC3 - Parameters

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Wartsendage.

Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Wartsendage.

PC3 - Parameter differences